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Evaluation of spectra

a spectra and spectrometer technology, applied in the field of spectra evaluation, can solve the problems of limited structural determination by nuclear magnetic resonance (nmr) spectroscopy, dramatic affect on protein solubility,

Inactive Publication Date: 2007-08-09
AFFINIUM PHARMA
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

"The present patent is about methods and systems for evaluating spectra of biological molecules, such as proteins, nucleic acids, and small molecules. The methods involve creating a training set based on a plurality of spectra, associating the spectra with categories, scoring the spectral parameters of the spectra in the categories, and comparing the spectral parameters of sample spectra to the scored parameters of the training set. This allows for the classification of the sample spectra into one of the categories. The computer product described in the patent is a computer-readable medium with instructions for causing a processor to perform the scoring and comparison steps. The technical effect of this patent is the improved ability to evaluate and analyze biological molecule spectra."

Problems solved by technology

One research challenge is to determine samples and / or solution conditions amenable for analysis by a particular structural method.
For example, structural determination by Nuclear Magnetic Resonance (NMR) spectroscopy may be limited by the size and solubility properties of a sample.
Moreover, it is known that, in certain instances, even small changes in the amino acid sequence of a protein may lead to dramatic affects on protein solubility.

Method used

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Examples

Experimental program
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example 1

Protein Purification of 15N Labeled Polypeptides

[0124] The cells, harboring a plasmid each with a nucleic acid encoding a polypeptide of the invention, are inoculated into 2 L of M9 minimal media (containing 15N isotope, 0.48 g / L 15NH4Cl) in a 6 L Erlenmeyer flask. The minimal media is supplemented with 0.01 mM ZnSO4, 0.1 mM CaCl2, 1 mM MgSO4, 5 mg / L Thiamine.HCl, and 0.4% glucose. The 2 L culture is grown at 37° C. and 200 rpm to an OD600 of between 0.7-0.8. The cultures are then induced with 0.5 mM IPTG in each culture and allowed to shake at 15° C. for 14 hours. The cells are harvested by centrifugation and the cell pellets are resuspended in 15 mL cold binding buffer each and 100 μl of protease inhibitor and flash frozen. The protein is then purified as described below from each of resuspended pellets.

[0125] Alternatively, the freshly transformed cells, harboring a plasmid each with the gene of interest, is inoculated into 10 mL of M9 media (with 15N isotope) and supplemented ...

example 2

Acquisition of HSQC NMR Spectra on Multiple Proteins

[0130] NMR experiments were performed on a Bruker Avance 600-MHz spectrometer equipped with a 5-mm triple-resonance cryo-probe head at 298 K. NMR samples were typically prepared in 500 μl of 90% H2O-10% D2O buffer containing 500 mM NaCl, 10 mM HEPES buffer at pH 7.5 (pH reading is not corrected for isotopic effects). The two dimensional (1H, 15N)HSQC experiments were acquired using the pulse sequence described by Davis et al. (J. Magn. Reson. 98: 207-216 (1992)), Grzesiek and Bax (J. Am. Chem. Soc. 115: 12593-12594 (1993)) with water suppression by flip-back pulses. The sweep width was 14 ppm and 45 ppm in the 1H and 15N dimensions, respectively. The 1H carrier was set at 600.1324 MHz, while the 15N carrier at 60.1778 MHz. The size of the HSQC spectra gave a 1024×128 real data matrix. The spectra were processed on a Ultra 5 computer from SUN Microsystems using NMRPipe software (Delaglio et al., J. Biomol. NMR 6: 277-293 (1995)).

example 3

Manual Categorization of HSQC NMR Spectra of the Training Set

[0131] The protein spectra obtained in Example 2 (FIG. 2) are associated with one of the following four categories: (a) good, Protein 1 and 2, (b) promising, Protein 3 and 4, (c) unfolded, protein 5 and 6, and (d) poor, Protein 7 and 8. The association takes into account the chemical shift dispersion in both proton and nitrogen dimension, intensity and line-width of the peaks and number of peaks observed versus the number of peaks expected which equals the number of non-proline residues in the protein (excluding side chain NH2 groups). Typically, a 1H chemical shift range from 5.5 to 12 ppm and a 15N chemical shift range from 98 to 140 ppm is considered.

TABLE 1HSQC spectra ofClassificationProtein 1GoodProtein 2GoodProtein 3PromisingProtein 4PromisingProtein 5UnfoldedProtein 6UnfoldedProtein 7PoorProtein 8Poor

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Abstract

Systems, methods, products and analyzers that allow evaluation of spectra of molecules, including proteins, nucleic acids and small molecules, are provided. The spectra that may be evaluated by the systems, methods, products and analyzers include, for example, spectra collected by the techniques of NMR, mass spectrometry, infrared and RAMAN spectroscopy, chromatography, etc.

Description

RELATED APPLICATIONS [0001] This application claims the benefit of priority to U.S. Provisional Patent Application No. 60 / 471,201, filed on May 16, 2003, which application is hereby incorporated by reference in its entirety.INTRODUCTION [0002] Genomic sequence information for many organisms is now available. However, knowledge of the complete genomic sequence is only the first step towards understanding the function of encoded proteins and nucleic acid molecules. Structural information acquired on a genome wide level in all likelihood will provide valuable information for predicting the rules that govern the formation of secondary and tertiary structure in proteins and nucleic acids. Such insight should prove useful in understanding the biochemical function of molecules and should provide an opportunity for rapid progress in the identification of targets for therapeutics. [0003] Availability of sequence information makes it possible to isolate biological molecules for structural det...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12Q1/68G06F19/00G01N24/08G01N33/48G01N37/00
CPCG01N24/087G01N24/088G06K9/00536G01R33/465G01R33/4625G06F2218/12
Inventor ARROWSMITH, CHERYLGRISHAEV, ALEXANDER
Owner AFFINIUM PHARMA
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